Genome-wide and molecular evolution analyses of the phospholipase D gene family in Poplar and Grape

BACKGROUND: The Phospholipase D (PLD) family plays an important role in the regulation of cellular processes in plants, including abscisic acid signaling, programmed cell death, root hair patterning, root growth, freezing tolerance and other stress responses. PLD genes constitute an important gene family in higher plants. However, until now our knowledge concerning the PLD gene family members and their evolutionary relationship in woody plants such as Poplar and Grape has been limited. RESULTS: In this study, we have provided a genome-wide analysis of the PLD gene family in Poplar and Grape. Eighteen and eleven members of the PLD gene family were identified in Poplar and Grape respectively. Phylogenetic and gene structure analyses showed that the PLD gene family can be divided into 6 subgroups: α, β/γ, δ, ε, ζ, and φ, and that the 6 PLD subgroups originated from 4 original ancestors through a series of gene duplications. Interestingly, the majority of the PLD genes from both Poplar (76.5%, 13/17) and Grape (90.9%, 10/11) clustered closely together in the phylogenetic tree to the extent that their evolutionary relationship appears more tightly linked to each other, at least in terms of the PLD gene family, than it does to either Arabidopsis or rice. Five pairs of duplicated PLD genes were identified in Poplar, more than those in Grape, suggesting that frequent gene duplications occurred after these species diverged, resulting in a rapid expansion of the PLD gene family in Poplar. The majority of the gene duplications in Poplar were caused by segmental duplication and were distinct from those in Arabidopsis, rice and Grape. Additionally, the gene duplications in Poplar were estimated to have occurred from 11.31 to 13.76 million years ago, which are later than those that occurred in the other three plant species. Adaptive evolution analysis showed that positive selection contributed to the evolution of the PXPH- and SP-PLDs, whereas purifying selection has driven the evolution of C2-PLDs that contain a C2 domain in their N-terminal. Analyses have shown that the C2-PLDs generally contain 23 motifs, more than 17 motifs in PXPH-PLDs that contain PX and PH domains in N-terminal. Among these identified motifs, eight, (6, 8, 5, 4, 3, 14, 1 and 19) were shared by both the C2- and PXPH-PLD subfamilies, implying that they may be necessary for PLD function. Five of these shared motifs are located in the central region of the proteins, thus strongly suggesting that this region containing a HKD domain (named after three conserved H, K and D residues) plays a key role in the lipase activity of the PLDs. CONCLUSION: As a first step towards genome wide analyses of the PLD genes in woody plants, our results provide valuable information for increasing our understanding of the function and evolution of the PLD gene family in higher plants.